GSM7384996: Rice-scATAC-SAM-Rep2; Oryza sativa; ATAC-seq
A total of 20,000 nuclei from each rice sample were pooled for single-cell multiome library generation using the 10X genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. The nuclei were counted by Luna FL (Logos Biosystems). GEMs were generated using the 10X Chromium Controller with one lane of GEM chip (Chromium Next GEM Chip J) for each sample. scATAC and gene expression libraries from each pool were generated Glbizzia Biosciences following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide. In brief, nuclei were incubated in a transposition mix that includes transposases that enter the nuclei and fragment DNA in open regions of chromatin, while simultaneously adaptor sequences are added to the fragments. Single Cell Multiome ATAC + GEX Gel Beads capture the adaptor sequences on DNA fragments as well as the poly-A tail of mRNA and GEMs are generated and incubated, resulting in 10x barcoded DNA from the transposed DNA (for ATAC) and 10x barcoded, full-length cDNA from poly-adenylated mRNA (for GEX). cDNA was then purified, amplified and sequenced per the manufacturer's recommendations (10x Genomics). The libraries were sequenced with Illumina NovaSeq 6000 under the modes of PE150 (scRNA-seq library) and PE50 (scATAC-seq library).